Quast Evaluator

Depends on Quast version 3.2

Install

Pandoc (version > 1.17) must be installed

1.Clone this repository with git clone https://github.com/pbelmann/quast-evaluator.git

2.Change working directory: cd quast-evaluator

3.Run R -e 'install.packages("packrat" , repos="http://cran.us.r-project.org"); packrat::restore()'

User Guide

Quast Evaluator has two modes:

'new' Mode

This mode lets you collect quast results from different quast output directories.

Run

Rscript quast_evaluator_cli.r new /path/to/assemblers.tsv /path/to/info.tsv -o /path/to/output/directory

where assemblers.tsv and info.tsv must have the following columns:

• assemblers.tsv:

name	assembler       path	group
assembler1	jolly_euclid_1  /home/belmann/projects/quast-evaluator/tests/testthat/data/assembler1	1
assembler2	angry_newton_2  /home/belmann/projects/quast-evaluator/tests/testthat/data/assembler2	2

where

• /home/belmann/projects/quast-evaluator/tests/testthat/data/assembler1 must contain the directories runs_per_reference and combined_reference

• name is the assembler name that will be shown in the plots

• assembler is the name of the assembler provided to metaquast.

• info.tsv:

id              path	        group	length	mapping	
1030752.gt1kb   1030752.gt1kb   strain	1200	43000
1030755.gt1kb   1030755.gt1kb   strain	2300	89999
1030836.gt1kb   1030836.gt1kb   evolved	4500	76666
1030878.gt1kb   1030878.gt1kb   evolved	8999	50000

where

• path is a directory inside the runs_per_reference directory.
• id is a uniq identifier
• group is an identfier which groups different references
• length is the length of the reference
• mapping how many reads are mapped to the specific reference

'reuse' Mode

This mode lets you reuse tsv files produced by the 'new' mode.

Run

Rscript quast_evaluator_cli.r reuse /path/to/combined_ref_data.tsv /path/to/ref_data.tsv -o /path/to/output/directory

where combined_ref_data.tsv and ref_data.tsv have the columns stated in these example files: tests/testthat/data/ref_data.tsv and tests/testthat/data/combined_ref_data.tsv

Further Parameters:

• '-c /path/to/plot.conf' This file allows you to define min and max for each plot individually. The here for an example.

Example

See tests

Developer Guide

You can run tests with

R -e 'devtools::test()'

Please use this if you want to propose a Pull Request.